Dear All,
I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.
I tried g_trjconv with application of -pbc mol -ur compact options on
untruncated(100ns) trajectory. The results came as:
*ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) =
1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 = 3.03095Q
= 0--------------------------------------------------Type
Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward 0.001
1793.775 23.259 3.03095*
When I tried the same with the original unconverted trajectory(without
g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*.
*My question is ,*
*Which value should I take, since application of pbc gives a different
value than that of the original trajectory value of lifetime.*
I would be very grateful for your help.
Looking forward to your suggestions
Yours sincerely
Apramita Chand